assertEquals(2, seq.findIndex(seq.getStart()));
// no hidden columns
- assertEquals(
- Arrays.toString(new int[]
- { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ assertEquals(seq.findIndex(seq.getStart()) - 1, cs.locateVisibleBoundsOfSequence(seq));
// hidden column on gap after end of sequence - should not affect bounds
colsel.hideSelectedColumns(13, al.getHiddenColumns());
- assertEquals(
- Arrays.toString(new int[]
- { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ assertEquals(seq.findIndex(seq.getStart()) - 1,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
// hidden column on gap before beginning of sequence - should vis bounds by
// one
colsel.hideSelectedColumns(0, al.getHiddenColumns());
- assertEquals(
- Arrays.toString(new int[]
- { seq.findIndex(seq.getStart()) - 2, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ assertEquals(seq.findIndex(seq.getStart()) - 2,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
// hide columns around most of sequence - leave one residue remaining
cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
{ seq })[0]);
- assertEquals(
- Arrays.toString(
- new int[]
- { 1, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ assertEquals(1, cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
// hide whole sequence - should just get location of hidden region
// containing sequence
cs.hideColumns(1, 11);
- assertEquals(
- Arrays.toString(
- new int[]
- { 0, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 15);
- assertEquals(Arrays
- .toString(new int[]
- { 0, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(7, 17);
- assertEquals(
- Arrays.toString(
- new int[]
- { 0, seq2.findIndex(seq2.getStart()) - 1,
- seq2.findIndex(seq2.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq2));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(3, 17);
- assertEquals(
- Arrays.toString(
- new int[]
- { 0, seq2.findIndex(seq2.getStart()) - 1,
- seq2.findIndex(seq2.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq2));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(3, 19);
- assertEquals(
- Arrays.toString(
- new int[]
- { 0, seq2.findIndex(seq2.getStart()) - 1,
- seq2.findIndex(seq2.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq2));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 0);
- int[] test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 1);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(1,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 2);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(1, 1);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 2, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(2,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(1, 2);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(1,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(1, 3);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(1,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 2);
cs.hideColumns(5, 6);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 2);
cs.hideColumns(5, 6);
cs.hideColumns(9, 10);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 2);
cs.hideColumns(7, 11);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
cs.hideColumns(7, 11);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(1,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
cs.hideColumns(7, 12);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(1,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(1, 11);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 12);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 4);
cs.hideColumns(6, 12);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 1);
cs.hideColumns(3, 12);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleBoundsOfSequence(seq));
- // These tests cover different behaviour to original
- // locateVisibleBoundsOfSequence
- // Previously first values of each were 3,9 and 6 respectively.
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(3, 14);
cs.hideColumns(17, 19);
- assertEquals(
- Arrays.toString(
- new int[]
- { 3, seq2.findIndex(seq2.getStart()) - 1,
- seq2.findIndex(seq2.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
+ assertEquals(3,cs.locateVisibleBoundsOfSequence(seq2));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(3, 7);
cs.hideColumns(9, 14);
cs.hideColumns(17, 19);
- assertEquals(
- Arrays.toString(
- new int[]
- { 9, seq2.findIndex(seq2.getStart()) - 1,
- seq2.findIndex(seq2.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
+ assertEquals(9,cs.locateVisibleBoundsOfSequence(seq2));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 1);
cs.hideColumns(3, 4);
cs.hideColumns(6, 8);
cs.hideColumns(10, 12);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 6, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(6, cs.locateVisibleBoundsOfSequence(seq));
}
cs.hideInsertionsFor(al.getSequenceAt(0));
assertEquals("G", ""
+ al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9)));
-
}
@Test(groups = { "Functional" })